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... on RNA level), but further there is amplification of the signal (there can be thousands copies of each mRNA, each giving rise to hundreds of protein molecules), also, during replication of DNA the protein synthesis would have to be shut down and there could be other reasons. But as said, ...

... tried to differentiate the two and left me pretty confused. From my understanding, increased gene expression will result in an increase in the protein product that a gene is coding for. Meaning that if you increased expression of a gene that codes for an enzyme, it would result in upregulation ...

That's a reasonable idea. I can imagine a ribosome directly binding to DNA to translate the DNA codons directly into protein. We can't really tell why that didn't happen, as much of the early development of life occurred far in the past and left no evidence of the steps in the process; ...

... this is what my text says on the basic diagram "This Scientists generated mouse embryos in which the Pitx1 gene was mutated, making the Pitx1 protein non-functional from the start of mouse development. The images of the Pitx1 “knockout” mouse shown below on the right reveal striking differences ...